The whole point of a snap cap is to have a primer like surface for the striker to land on and avoid damage to the fireing pin. If you drill out the primer you negate any advantage. I have read that folks will pop the speng primer and fill the primer pocket flush with a hot glue gun. Not tried it myself.
If you want to make dummy rounds just pull the bullet, dump the powder and reset the bullet I would not.drill the primer on a live round. Sounds very Darwinesque.